Mercurial > repos > artbio > sr_bowtie
comparison sRbowtie.xml @ 5:0281bb245635 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 9112ef4fcf1fdac850fcc58195d39ca3d0e34857
| author | artbio |
|---|---|
| date | Wed, 26 Sep 2018 10:47:19 -0400 |
| parents | 3c9d01ebc56d |
| children | e4a05086ea02 |
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| 4:3c9d01ebc56d | 5:0281bb245635 |
|---|---|
| 1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.1.0"> | 1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.1.1"> |
| 2 <description>for small RNA short reads</description> | 2 <description>for small RNA short reads</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.1.2=py27_0">bowtie</requirement> | 4 <requirement type="package" version="1.1.2=py27_0">bowtie</requirement> |
| 5 <requirement type="package" version="1.2">samtools</requirement> | 5 <requirement type="package" version="1.2">samtools</requirement> |
| 6 </requirements> | 6 </requirements> |
| 122 </action> | 122 </action> |
| 123 </when> | 123 </when> |
| 124 </conditional> | 124 </conditional> |
| 125 </actions> | 125 </actions> |
| 126 </data> | 126 </data> |
| 127 <data format="fastqsanger" label="Matched reads" name="aligned"> | 127 <data format_source="input" label="Matched reads" name="aligned"> |
| 128 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter> | 128 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter> |
| 129 <actions> | |
| 130 <action type="format"> | |
| 131 <option type="from_param" name="input" param_attribute="ext" /> | |
| 132 </action> | |
| 133 </actions> | |
| 134 </data> | 129 </data> |
| 135 <data format="fastqsanger" label="Unmatched reads" name="unaligned"> | 130 <data format_source="input" label="Unmatched reads" name="unaligned"> |
| 136 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter> | 131 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter> |
| 137 <actions> | |
| 138 <action type="format"> | |
| 139 <option type="from_param" name="input" param_attribute="ext" /> | |
| 140 </action> | |
| 141 </actions> | |
| 142 </data> | 132 </data> |
| 143 </outputs> | 133 </outputs> |
| 144 <tests> | 134 <tests> |
| 145 <test> | 135 <test> |
| 146 <param name="genomeSource" value="history" /> | 136 <param name="genomeSource" value="history" /> |
| 164 <param name="genomeSource" value="history" /> | 154 <param name="genomeSource" value="history" /> |
| 165 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | 155 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> |
| 166 <param name="method" value="unique" /> | 156 <param name="method" value="unique" /> |
| 167 <param ftype="fastqsanger" name="input" value="input.fastqsanger" /> | 157 <param ftype="fastqsanger" name="input" value="input.fastqsanger" /> |
| 168 <param name="v_mismatches" value="1" /> | 158 <param name="v_mismatches" value="1" /> |
| 159 <param name="additional_fasta" value="al" /> | |
| 169 <param name="output_format" value="bam" /> | 160 <param name="output_format" value="bam" /> |
| 170 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> | 161 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> |
| 162 <output file="al.fastqsanger" ftype="fastqsanger" name="aligned" /> | |
| 171 </test> | 163 </test> |
| 172 <test> | 164 <test> |
| 173 <param name="genomeSource" value="history" /> | 165 <param name="genomeSource" value="history" /> |
| 174 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> | 166 <param ftype="fasta" name="ownFile" value="297_reference.fa" /> |
| 175 <param name="method" value="multiple" /> | 167 <param name="method" value="multiple" /> |